I've shape a few boards and have used probox, futures, and FCS fusions. Hands down probox are the most adjustable. Futures are the least. They are all easy as pie to install if you have the jigs. As a semi shaper I don't like straight lines. So futures seem like there are a lot of straight lines, meaning 4 failure areas per fin. Probox and fusions have no straight lines so zero fail points.
Now about the two size future boxes. It sounds like a mistake by your glasser or shaper. The more shallow box should be used as the rear boxes or box due to the need to fit in the more foiled or thin tails. It should only fit rear fin bases.
FCS just happen to be first to market and first to be knocked off. In side the base slots should actually say FCS if you look down in them on older models, new ones have logo on the outside. Because they were first to the market they are world wide so if you're in a third world country, you have a better chance to get a blow out fixed.
True Ames and rainbow are great companies who offer more templates if you can't find an FCS / futures mirror. Like futures controllers, rainbow makes an FCS base match.
I'm a fin whore and by no means an expert so try all that you can, that's what I love doing.
I like Futures, esp. the Tokoro fins, but I have noticed the boxes seem to hold water, anybody else notice this?
It tends to cause the set screws to develop corrosion.